MapScape

MapScape visualizes the spatial distribution of tumour clones by integrating clonal phylogenies, clonal prevalence estimates, anatomical reference images, pixel coordinates, and mutation data to explore clonal evolution in cancer.

Key Features:

• Core inputs: Accepts a clonal phylogeny describing evolutionary relationships among clones, clonal prevalence estimates across sampled anatomical sites, a reference image (e.g., medical imaging or schematic anatomical drawing), and pixel coordinates mapping each tumour sample to the image.
• Optional inputs: Supports clone-level mutation tables and variant allele frequencies for enhanced interpretability.
• Integration of phylogeny and prevalence: Maps clonal hierarchies and clonal prevalences onto anatomical locations to relate evolutionary relationships to spatial distribution.
• Per-sample visual encodings: Produces a cellular aggregate plot showing proportional abundance of clones within each sample and a phylogenetic skeleton highlighting the subset of clones present in that sample.
• Annotated anatomical output: Generates an annotated anatomical image with samples positioned at provided pixel coordinates.
• Analytical capabilities: Enables inspection of spatial heterogeneity, clonal mixing, metastatic seeding patterns, and anatomical constraints on tumour evolution.

Scientific Applications:

• Spatial clonal mapping: Characterize the distribution of genetically distinct tumour clones across anatomical sites.
• Metastatic seeding inference: Examine clonal presence across samples to infer putative metastatic routes.
• Clonal heterogeneity and mixing: Assess intra-sample clonal composition and clonal mixing across sites.
• Treatment resistance and progression hypotheses: Support generation of hypotheses regarding treatment resistance, tumour progression, and metastatic spread.
• Complementing time-resolved analyses: Provide a spatial perspective that complements time-resolved tools such as TimeScape.

Methodology:

Takes as input a clonal phylogeny, clonal prevalence estimates per sampled site, a reference image and pixel coordinates, and optionally clone-level mutation tables and variant allele frequencies, and produces an annotated anatomical image with per-sample cellular aggregate plots and phylogenetic skeletons that map clones to anatomical coordinates.